18 BBY/2IY: Supreme commander of the Imperial Fleet, Lord Vader ordered the execution of Queen Apailana of Naboo on the charges of committing treason against the empire by harboring fugitive . The 501st was sent to eliminate her but the battle became a disaster the empire for a number of unexpected setbacks:
On the land the 501st was shocked to see that the defenders of Naboo was leaded by their former brethren's from the from the famed Torrent company, the most veteran company of the 501st under the command of the traitors captain CT-7567 "Rex", the former second-in-command under Lord Vader. Under his command the Naboo defenders put up a deadly resistance and then lunched an even more deadly counterattack that drove them from the planet. In the bloody engagement, the 501st lost an entire battalion, entirely composed of veteran troops from the clone wars and Operation: Knightfall.

18 BBY/ 2IY: Supreme commander of the Imperial Fleet, Lord Vader ordered the execution of Queen Apailana's of Naboo on the charges of committing treason against the empire by harboring Jedi fugitive. The 501st was sent to eliminate her but the battle became a disaster the empire for a number of unexpected setbacks:
On the land the 501st was shocked to see that the defenders of Naboo was leaded by their former brethren's from the from the famed Torrent company, the most veteran company of the 501st under the command of the traitors captain CT-7567 "Rex", the former second-in-command of lord Vader. Under his command the Naboo defenders put up a deadly resistance and then lunched an even more deadly counterattack that drove them off from the planate. In the bloody engagement, the 501st lost an entire battalion, entirely composed of veteran troops from the clone wars and Operation: Kinghtfall.
In space, the imperial HIGHCOM ordered commander of the fleet to execute Base Delta Zero on planet Naboo. However as soon as the fleet entered bombardment position, three Lucrehulk-class battleship jumps out of nowhere and attacked the imperial fleet. The imperial's, caught completely off-guard, suffers heavy losses and retreats. The Lucrehulk's than too quickly jumps away from the system. In this short but devastating space battle, the empire lost no less than 20 warship's of which 6 of them were brand new Imperial I-class star destroyers and the strength of the 501st was dropped down to three regiments. This badly weakened the imperial hold of this sector and the garrisoning forces became helpless when Queen Apailana's ignited a sector wide revolt. This disastrous defeat setback empires many operations' for years as they begun to consolidate their positions and gather forces for a decisive counterattack on the Chommell sector, which is now declared independence and re-equipped themselves with many clone wars ship and equipment that were mothballed in the Aostro'gar system by the empire, including one Mandator II class star dreadnought that was, unfortunately for the empire, was undergoing refit on one of Aostro'gar's shipyards.17 BBY/ 3IY: The Empire received rumors that a former CIS engineer is building a droid army on planet Mustafer. Due to their recent defeat and preparation for their invasion on the Chommell sector, the imperial HIGHCOM decided to send a single Victory-II class star destroyer under the command of the newly graduated captain Tyber zann to investigate. However the ship disappeared with no tress with only a single distress call saying that they are being attacked by ships from Corellian Security Force. The HIGHCOM, eager to make an example to the galaxy at large, ordered the Imperial troop to execute Diktat Dupas Thomree and kill all CorSec command personals. However the massage was intercepted by Bothan spies and was relayed to the Dupas. Dupas, upon receiving the massage decided that it was no longer beneficial for him to work for the empire and declared the entire Corellian sector independed and free from Imperial control. The small imperial garrison forces were wiped out by CorSec and Corellians. The Corellianst han started to produce new ships and stared to reactivate multiple fleet's equivalent of clone wars era ships that has been abounded or mothballed by the empire on the system.
Two week after this event, the Empire, desperate to make an example, declared all signees of the Delegation of 2000 traitors and ordered to execute not only themselves, but their families as well. While nearly two third of the senators were was successfully wiped out to their roots, the surviving senators took refuge in planet Alderaan and decided that the time of negotiations is over and it is time to take direct action against the Empire. They sparked what became known as the "tri system rebellion". The Bothan, Brema and Alderaan sector altogether started a successful organized revolution from their imperial occupation and declared independence. Only a day after the rebellion, they send diplomats to both the Corellian and Chommell and singed the famous, or rather, from the Imperial point of view, the infamous "Corellian treaty". With the treaty, all of the sectors became united under the banner of the "Republic constitutional authority" or RCA and started to co-operate with each other. Ships from Corellia and Sullust stated to re-enforce all other sector fleets, the massive war factories of Alderaan and Aostro'gar started to produce counless machine of wars and the Bothan's stared to wreak havoc on Imperial supply and logistics using their vast spy network and saboteurs. Only days after its formation, many other independent worlds and system declared independence and joined the RCA.
One mount after the establishment of the RCA, the Empire briefly lost contact with their base in kamino sector. However they soon reestablished contact and said they had to deal with a rebellion attempt. Two days later a similar incident happened on the Calamari sector, although this time the delay was a little longer. Both of them were ignored by imperial HIGHCOM as they were constantly getting reports of similar incidences were happing all over their territories.16 BBY/ 4IY: The empire took the initiative destroy the RCA by lunching an all out strike against the most lightly defended sector of sector of the all 5 rebellious sectors, the Chommell sector. While the RCA forces put up a deadly resistance, they soon pushed to the breaking point by the sheer might of the Imperial fleet. When all hope was seems lost for the RCA and they were about lose control of the Chommell sector , the Imperial forces was suddenly attack by multiple unknown fleets of ships all over the entire sector the Empire once again caught completely off guard, performs a hastily retreat. After the battles was over, the fleets ware revealed to be Mon- calamari origin and the troops manning them were clones recently created by kaminouns. Apparently, the kaminouns had secretly lunched a covert sector-wide uprising using their newly created clone army; however they used faked transmissions to fool the imperial HIGHCOM to thinking that their forces were still in control. Then having their clone army disguised as imperial re-enforcement, they assaulted and liberated the Mon- calamari sector. The introduction of these two forces sparked the first RCA diplomatic crisis. While the Mon- calamariuns were a welcoming sight, the idea of introducing the clones to the RCA Armed forces was received with mixed repose by the RCA senators. While some of the senators were please to have an un-questionably loyal army that was virtually infinite in numbers, others question their moral stands as they follows any orders, good or bad, without hesitation as seen during the final days of the Clone wars.
While the senators of the RCA senate continues to bikers about intriguing clones to their defense forces, the Imperial fleet, still nowhere out of the fight, prepared for another offensive against RCA, this time involving all of their surviving super capitals. As they do RCA units nearly all of their fleets with the exceptions that of the clones for a quick retaliation strike on the imperial shipyards over Kuat. However, unknown to them, that is also the same place where the imperial armada is gathering for the second offensive.
As soon as the RCA fleet jumps over the shipyards of the Kuat, both sides were caught completely surprised and the imperial were once again caught off-guard with 1-3rd of their vessel still in the dry dock. However they still have enough battle-ready ships to match the RCA fleet and the space over kuat soon became a deadly battlezone. After a battle that lasted for nearly 8 hours, the nearly devastated RCA fleets withdrew from Kuat, with the secured knowledge that they have inflicted far more damage to the Empire and denied the imperials the use of Kuat's shipyards for quite some time, thus achieving a strategic victory. However, as soon as they came back to their territory, their joy of victory shattered as they learned that many of their shipyards along with majority of their military facilities are destroyed by a massive droid armada. Others only survived thanks to the action of the clone forces they left behind. They later learned similar event happened in the Imperial territory and the imperial managed to destroy the armada but only after suffering heavy damage to their war machine.Two days later, the attacks revealed to be committed by the "Consortium of Independent Sectors" lead by a "Supreme Commander of the Consortium Forces" Tyber Zann, as he transmitted a galaxy-wide transmission calming responsibility for the attacks and calling all former Confederacy worlds to join the Consortium to "Fight the Tyrannical and oppressive Empire and RCA to ensure their safety and sovereignty". This lead to many worlds, both Imperial and RCA, to break away from their respecting factions and join the new CIS. This event even more badly hampered both factions ability to wage war and forced them to focus on recovering their losses. This was exactly what Tyber Zann wanted as this bought him the Time necessary to prepare the dormant CIS war engine against the galaxy.As all the faction started to recover their losses, they started to perform radical changes and expansions to their military forces. The Empire, knowing that they are likely to face Fett-clones troopers fielded by RCA, decided to consume all their remaining clone wars era clones to stromtrooper corps and transform it to a completely independent military brunch, complete with their own ships and equipment. The Emperor Plapatine decided that this way he can have his best and most loyal and elite forces ready to strike anywhere anytime he desires. He also charged his apprentice, Darth Vader with "Acolyte Program". The purpose of this program was to gather force sensitive throughout the galaxy, and teach them the ways of Sith , therefore giving him a force that can properly counter the resurgence Jedi order that surely RCA will help to rebuild.When the Consortium and RCA learned about the changes they also stared prepare their forces accordingly. In this particular issue, the Consortium faced a problem. Although they already maintain an elite droid forces consisting of lethal IG-100 MagnaGuards and BX-series droid commandos, they had nothing to counter the Jedi or the Sith. With that in mind, Tyber Zann contacted the Death watch Pre Vizsla, the leader of the in-famous renegade faction of Mandaloreuns. He insured that in-exchange of his forces loyalty to the Consortium; he will help him to take over Mandalore. Vizsla, skeptical due to his earlier bitter experience with the CIS, told him he will only accept the deal after Mandalore is his control. Tyber accepted and send him enough forces to lunch a successful coup d'état and take over the planet. With Mandalore under his control, Vizsla kept his word and committed his forces to the CIS. This solved Zann's issue with the Jedi and Sith froces as now he has a force under his command which has a legendary reputation for fighting both the Jedi and the Sith.The RCA, on the other hand, face a different kind of problem. While the RCA had Jedi order to fight the Sith and an impressive collection of elite forces like the Clone Commandoes and the new Rail-Class Advance Recon Commandoes, they didn't had the people's necessary to harness and use the full potential of this near uncontrollable free-thinking forces of elite troops. However, their problem solved as the Consortium sparked the Death watch lead coup on Mandalore, driving off the Mandaloreun protectors and the former members of the Cuy'val Dar, including the former Null-Class Advance Recon Commandoes. Furious to take back their home, members of the Cuy'val Dar and protectors contacted and proposed a deal to the RCA, that if the RCA help them to liberate the Mandalore, they will help the train and maintain their special forces to their most lethal capacity. Moreover, of the RCA provides a cure for accelerated aging of the Null-Class Advance Recon Commandoes, they will take command of their elite forces and make sure that they "get the job done". The offer was too good for the RCA to pass up, and only within 16 hours of receiving their proposal, the RCA sent them an approval massage with a request to send them a senator to represent their "government-in-exile" on the RCA senate, which was accepted. Although this were not the only change the RCA implemented on their forces. In land, the RCA adopted a "quality over quantity" policy for rebuilding their forces. Making the highly trained clones their frontline infantry while their birth born recruits re-assigned for defensive and second line duty‘s. In space the RCA know all too well that they simply cannot match up with the ship production capacity of the Empire and Consortium and decided to make their ship capable of engaging multiple ships at once. While the RCA ship builder started to draw up new ship designed capable of doing just that it was soon clear that it will take years for those designs to come to life, years that the RCA does not have. In knowledge of this the RCA senate authorized "Project Reborn" a program to utilize some of the most famous starships designs throughout the history and re-fitted them with the bleeding edge technology's. While this was only meant to be a stop-gap, the early prototype were found to be so promising the RCA soon increased funding in the project, and stated to integrate many older even ancient ship designs into their growing navy.15 BBY/ 5IY: All three factions have successfully recovered enough to continue their war against each other. One side waits for the others to make the first strike and spark the Second Clone Wars. What will happen next? Which side will triumph? Only the commanders can decide.

pretty good story i must say, however you kinda lost me at Alderaan's war machine, I mean at the time Alderaan was still recovering from the horrors of the first clone wars, and declared the planet weapons free. I cant see them rushing to build another "war machine" just my 2 cents :)

Alright fair enough this is before they dismantle, but then how do they react to the CIS's Atrocities on planet, does the whole planet just get one giant dose of blood lust and decide to ram the empire/consortium a new hole? sorry im probably thinking into this to much xD

WoW... now this is a solid "what if" of Fanon Universe. but i have some questions.
The rebellion(RCA) that is now conformed by Clones, will still have some militians (Normal Rebel troopers as Cheap infantry/Not-Clones), also in space, you show up the Aurek Tactical Fighter, does this mean that the RCA will have some ships from the old republic like the hammerhead, preatorian and foray or these ships are TOO outdated to be part of a "moderm" army?

Here is a extract from the expanded part:
...In land, the RCA adopted a "quality over quantity" policy for rebuilding their forces. Making the highly trained clones their frontline infantry while their birth born recruits re-assigned for defensive and second line duty‘s. In space the RCA know all too well that they simply cannot match up with the ship production capacity of the Empire and Consortium and decided to make their ship capable of engaging multiple ships at once. While the RCA ship builder started to draw up new ship designed capable of doing just that it was soon clear that it will take years for those designs to come to life, years that the RCA does not have. In knowledge of this the RCA senate authorized "Project Reborn" a program to utilize some of the most famous starships designs throughout the history and re-fitted them with the bleeding edge technology's. While this was only meant to be a stop-gap, the early prototype were found to be so promising the RCA soon increased funding in the project, and stated to integrate many older even ancient ship designs into their growing navy.

Sorry about that. Did this in a hurry and didn't re-read it after I was done with it. And also I was suffering from a major back pain and cuts due to an accident. I am going to ask ΘsΘdeadly to Beta-read them from now on. Hopefully that will will cut down the number of typos.

well after reading this.... kudos to all of you. i shall follow this mod more closely now. at first i thought it was just another clone wars mod with a different backstory, but not anymore. i think that if lucasarts actually looked at these mods they would realize what creative minds people still have and consider recruting from moddb users xD